New variant of coronavirus discovered in Ontario deer

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A researcher attempts to take a sample from a white-tailed deer at a Texas A&M University wildlife center in College Station, Texas, on Feb. 2, 2022. (Sergio Flores/The New York Times)

Scientists have identified a new version of the coronavirus with a large number of mutations in white-tailed deer from southwestern Ontario, which may have been evolving in the animals since late 2020.

They also found a very similar viral sequence in a local person who had close contact with deer, the first evidence of possible deer-to-human transmission of the virus.

“The virus is evolving in deer and diverging in this species in a different way than it does in humans,” said Samira Mubareka, a virologist at the Sunnybrook Research Institute and the University of Toronto, who was one of the authors of the new study.

The report has not yet been published in a peer-reviewed journal, and there is no evidence that the deer variant is spreading among or posing a high risk to people. Preliminary laboratory experiments suggest that this variant is unlikely to evade human antibodies.

However, the paper was posted online just days following another team reported that the alpha variant may have continued to spread and evolve in Pennsylvania deer even following it had disappeared from human populations.

Together, the two studies suggest that the virus might be circulating among deer for long periods, raising the risk that the animals will become a long-term reservoir of the virus and the source of future variants.

Previous studies have revealed that the virus is widespread among white-tailed deer. Research suggests that humans have repeatedly infected deer and deer then passed it on to each other. How humans transmit the virus to deer remains a mystery, and until now, there has been no evidence that animals spread it to humans.

The Canada study was a collaboration involving more than twenty researchers from institutions across Ontario. Scientists collected nasal swabs and lymph node tissue samples from 300 white-tailed deer killed by hunters in Ontario between Nov. 1 and Dec. 31, 2021. Six percent of the animals, all of them from the Southwest from Ontario, tested positive for the virus, suggesting they had an active infection when they died.

The researchers sequenced the complete viral genomes of five infected deer and found a unique constellation of mutations that had not been previously documented. In all, 76 mutations (some of which had previously been found in infected deer, mink and other animals) differentiated the variant from the original version of the virus.

The deer samples were most closely related to viral samples taken from human patients in Michigan, not far from southwestern Ontario, in November and December 2020. They were also similar to samples taken from humans and mink in Michigan earlier that year. fall.

These findings, as well as the rate at which the virus accumulates mutations, suggest that the new variant may have diverged from known versions of the virus and been evolving undetected since late 2020.

However, its exact path is unclear. One possibility is that humans transmitted the virus directly to deer, and that the virus accumulated mutations as it spread among cervids. Another possibility is that the lineage evolved, at least in part, into another intermediate species (perhaps farmed or wild mink) which then passed it on to deer in some way.

“We don’t have all the pieces of the puzzle,” Suresh Kuchipudi, a Penn State veterinary microbiologist who was not involved in the research, said in an email. “We cannot rule out the involvement of an intermediate host.”

A viral sample collected from a human patient in southwestern Ontario in the fall of 2021 matched samples from deer. That person is known to have had “close contact” with them, according to investigators.

(They mightn’t reveal more details regarding the nature of this contact for privacy reasons, though Mubareka noted that people needn’t worry regarding incidental and indirect encounters, such as just a deer passing through their yard.)

The scientists caution that the sample size is small and that there is no conclusive evidence that the person contracted the virus from deer.

“We still don’t have enough information to confirm this deer-to-human spread,” said Roderick Gagne, a wildlife disease ecologist at the University of Pennsylvania School of Veterinary Medicine.

Early data suggests that existing vaccines should continue to protect once morest that variant. The vaccinated people’s antibodies were able to neutralize the pseudoviruses (harmless viruses that don’t replicate), which had been engineered to resemble the deer lineage, according to the scientists.

In the second study, scientists from the University of Pennsylvania Schools of Veterinary and Medicine analyzed nasal swabs from 93 deer that died in Pennsylvania in the fall and winter of 2021. 19 percent had an active virus infection. When the researchers sequenced seven of the samples, they found that five of the deer were infected with the delta variant, while two were infected with the alpha.

At the time the samples were collected, the delta variant was widespread among human inhabitants of the United States, but the alpha surge, which hit Americans in the spring of 2021, had long since faded.

“The alpha variant appears to persist in white-tailed deer even during the period when it does not circulate in humans,” said Eman Anis, a microbiologist at the University of Pennsylvania School of Veterinary Medicine, who co-authored the study. .

In fact, delta samples in deer were genetically similar to humans, suggesting that it had crossed species lines relatively recently, but the two alpha sequences had diverged more from the human variant. . (They were also very different from each other, suggesting that the variant had been introduced into the deer population at least twice.)

“The main conclusion would be that deer maintain contagion and infections within their populations,” explained Gagne, one of the authors of the Pennsylvania study. “So it’s not just a side effect of human-to-human transmission, the deer get infected and then it goes away.”

It is not known whether these variants will continue to circulate and evolve in deer, or what risk they pose to humans and other animals.